A high-content imaging system (HCIS) may be used to obtain a microscopy image of a biological sample. Such image may include a number of cells against a background field. Further, the HCIS may be used to obtain a series of microscopy images of the biological sample, wherein, for example, each image is obtained using a different focus point. Such series of microscopy images may be combined to develop a three-dimensional view of the biological sample. Such series of microscopy images may also be analyzed to segment and identify a portion of each such image that is associated with a particular cell. Such portions may then be combined to form a three-dimensional view of the particular cell, analyzed further to identify organelles within the three-dimensional cell body, and/or develop three-dimensional statistics of the three-dimensional cell body and/or the organelles therein.
A researcher may want to obtain statistics of cells that are present in the microscopy image or series of microscopy images. Such statistics may include a count of how may cells of a particular cell type are present in the image, the range of sizes (e.g., dimensions, volumes and surface areas) of such cells, the mean, median and mode of the sizes of such cells, how well the cell conforms to particular shape (e.g., sphericity), and the like. Further, the images may be analyzed to identify organelles within cells identified in such images and the statistics of such organelles may also be developed. Before any such statistics can be calculated, cells in the microscopy image must be segmented from the background and also from any debris present in the microscopy image.
An interactive image analysis system may be used to specify a sequence of image analysis steps and parameters for each step. Examples of image analysis steps include, for example, select an image captured using a particular illumination source, threshold the image, and apply one or more filters to the image. Example filters may include unsharp mask, a smoothing filter, and the like. After the sequence of image analysis steps and corresponding parameters are specified, measurements may be taken of the image that results when the specified the image analysis steps are applied. Such measurements include a count of different types of objects (e.g., cells or components of cells) that are present in the resulting image. Cohen et al., U.S. Pat. No. 8,577,079, entitled “IMAGE PROCESSING SYSTEM PROVIDING SELECTIVE ARRANGEMENT AND CONFIGURATION FOR AN IMAGE ANALYSIS SEQUENCE,” describes one such computer-implemented system for processing a selected image or series of images using multiple processing operations. The entire contents of this patent are incorporated herein by reference.